Does the CoE which HOMER calculates include excess electricity within the actual load supplied?  Ie if I have a system with big wind so producing huge volumes that are not used by the grid is the way you calculate CoE giving credit for that or not?
 

HOMER does not use excess electricity in its calculation for Cost of Energy (COE) which really refers to cost of electricity.

If you look of COE in the Help file you will see the equation used to calculate the cost of energy.  You will notice in the denominator of the formula there is absolutely no reference to the amount of electricity generated, rather the formula refers only to the sum of the electric loads that are served.

Excess electricity, by definition, is not serving a load and therefore does not make part of the COE metric.